Bispecific Binding Molecules That Target the Tumor Microenvironment and an Immune Checkpoint Protein

ABSTRACT

Bispecific binding proteins that bind IL-1β or IL-1R and a checkpoint protein are provided, together with methods of making the proteins. The checkpoint protein may be PD-1 or PD-L1. The binding proteins may have immunoglobulin-like structures that contain human Fab or scFv domains. A novel bispecific antibody format is provided. Methods of making the binding proteins are provided, together with pharmaceutical compositions containing the proteins. The binding proteins and pharmaceutical compositions may be used for treating or preventing diseases such as cancer.

This application claims priority to U.S. provisional application No. 62/827381, filed Apr. 1, 2019, the contents of which are hereby incorporated by reference in their entirety.

FIELD OF THE INVENTION

Bispecific binding molecules are provided that are useful for treating cancer and other diseases.

BACKGROUND

Immune checkpoints proteins act as immune system regulators and are a key part of the mechanism of self-tolerance. Inhibitory immune checkpoint proteins include: Programmed cell death protein 1 (PD-1); programmed cell death ligand 1 (PD-L1); Adenosine A2A receptor (A2AR); B7-H3 (CD276); B7-H4 (VTCN1), B and T Lymphocyte Attenuator (BTLA); Cytotoxic T-Lymphocyte-Associated protein 4 (CTLA-4, CD152); Indoleamine 2,3-dioxygenase (IDO); Killer-cell Immunoglobulin-like Receptor (KIR); Lymphocyte Activation Gene-3 (LAG3); Nicotinamide adenine dinucleotide phosphate NADPH oxidase isoform 2 (NOX2); T-cell Immunoglobulin domain and Mucin domain 3 (TIM-3); V-domain Ig suppressor of T cell activation (VISTA); Sialic acid-binding immunoglobulin-type lectin 7 (SIGLEC7, CD328); and Sialic acid-binding immunoglobulin-type lectin 9 (SIGLEC9, CD329).

Programmed cell death protein 1 (PD-1) is a receptor protein expressed on T-cells that acts as an immune checkpoint. PD-1 expression is unregulated on activated T cells as part of the mechanism of immune tolerance. The ligand for PD-1 is programmed cell death ligand 1 (PD-L1), and binding of PD-L1 to PD-1 transmits an inhibitory signal that reduces the activation and proliferation of antigen-specific T-cells in lymph nodes, and reduces apoptosis in regulatory T cells. Tumor cells often overexpress PD-L1 as a mechanism for avoiding immune surveillance. Monoclonal antibodies that inhibit binding between PD-1 and PD-L1—by binding either the ligand or receptor—have been shown to be effective either as monotherapy or in combination with other agents, in subpopulations of patients with a number of cancers, while being ineffective or refractory in many other cancers. Pembrolizumab is a humanized antibody that was first approved by the FDA in 2014 and that is used for treatment of a variety of cancers where the tumor cells express elevated PD-L1. Robert et al., N Engl. J Med. 372:2521-2532 (2015) Nivolumab is a fully human antibody that was first approved by the FDA in 2014 and also is used for treating a variety of cancers.

Tumor-associated macrophages (TAMs) are a class of immune cells present in high numbers in the tumor microenvironment (TME), and are associated with cancer-related inflammation. Expression of PD-1 on TAM cells has been shown to decrease macrophage phagocytosis of tumor cells and confers “immunity” on the tumor cells. Gordon et al, Nature 545:495 (2017).

Interleukin-1β (IL-1β) is a pro-inflammatory cytokine that is associated with chronic and acute inflammation and plays an important role in multiple inflammation-associated diseases. Elevated levels of IL-1β have also been shown to recruit TAM cells and myeloid-derived suppressor cells (MDSC) to the TME and to promote tumor growth and metastasis in breast cancer. Guo et al., Sci. Rep. 6, 36107; doi: 10.1038/srep36107 (2016). In other studies, lung lesions have been shown to be populated with TAM whose pro-tumor activity is up-regulated by activation of the NLRP3 inflammasome and the release of IL-1β. (Terlizzi et al., Oncotarget 7:58181 (2016)). Finally, IL-1β has been shown to promote a pro-tumor phenotype of TAM cells and the level of the cytokine has been correlated to tumor size & stage in renal cell carcinoma (Chittezhath et al., Immunity 41:815 (2014)).

In mice deficient in IL-1β, fewer animals developed tumors and tumor development was slower. Apte, et al., European Journal of Cancer, 42:751 (2006). Additionally, it was shown that the lung cancer risk genotype IL-1β-31TT results in increased expression of IL-1β, providing a microenvironment with elevated inflammatory stimuli and increase lung cancer risk. Bhat et al., Meta Gene 2:123 (2014). An IL-1 receptor antagonist was shown to suppress metastasis and tumor proliferation by inhibiting angiogenic factors such as VEGF and IL-8. Konishi et al., Oncology 68:138 (2005); Lewis et al, J. Transl. Med. 4:48 (2006). Canakinumab, a monoclonal antibody that inhibits IL-1β activity, has been shown to reduce incident lung cancer and lung cancer mortality. Ridker et al., Lancet, 390:P1833-1842, (2017).

Engineered bispecific monoclonal antibodies are non-naturally occurring proteins containing immunoglobulin domains that can simultaneously bind to two different types of antigen. Bispecific antibodies can be made in a variety of format and have been used, for example, for cancer immunotherapy and drug delivery. See, for example, Fan et al., J. Hemat. Oncol. 8:130 (2015); Brinkmann and Kontermann, mAbs 9:182 (2017); and Spiess et al., Molecular Immunology, 67: 95-106 (2015).

SUMMARY OF THE INVENTION

What is provided is a binding protein that may contain a first binding domain and a second binding domain, where the first binding domain specifically binds and inhibits activation of an immune checkpoint protein, and where the second binding domain specifically binds and inhibits the activity of IL-β or IL-1R. The immune checkpoint protein may be, for example, PD-1 or PD-L1. The first and second binding domains may contain immunoglobulin binding domains, such as human immunoglobulin binding domains. These binding protein may further contain a third binding domain that specifically binds and inhibits activation of an immune checkpoint protein, such as PD-1 or PD-L1, and a fourth binding domain that specifically binds and inhibits the activity of IL-β or IL-1R. The first and the third binding domains may contain the same CDR regions and the second and the fourth binding domains may contain the same CDR regions.

In one embodiment these protein the first binding domain may contain a) a heavy chain CDR1 of SEQ ID NO.:1; (b) a heavy chain CDR2 of SEQ ID NO.:2; (c) a heavy chain CDR3 of SEQ ID NO.:3; (d) a light chain CDR1 of SEQ ID NO.:4; (e) a light chain CDR2 of SEQ ID NO.:5; and (f) a light chain CDR3 of SEQ ID NO.:6. In this binding protein the first binding domain may contain the heavy chain variable region of SEQ ID NO: 37 and the light chain variable region of SEQ ID NO:38.

In another embodiment the first binding domain may contain a) a heavy chain CDR1 of SEQ ID NO.:7; (b) a heavy chain CDR2 of SEQ ID NO.8; (c) a heavy chain CDR3 of SEQ ID NO.:9; (d) a light chain CDR1 of SEQ ID NO.:10; (e) a light chain CDR2 of SEQ ID NO.:11; and (f) a light chain CDR3 of SEQ ID NO.:12. In this binding protein the first binding domain may contain the heavy chain variable region of SEQ ID NO: 39 and the light chain variable region of SEQ ID NO:40.

In a further embodiment the first binding domain may contain a) a heavy chain CDR1 of SEQ ID NO.:13; (b) a heavy chain CDR2 of SEQ ID NO.15; (c) a heavy chain CDR3 of SEQ ID NO.:15; (d) a light chain CDR1 of SEQ ID NO.:16; (e) a light chain CDR2 of SEQ ID NO.:17; and (f) a light chain CDR3 of SEQ ID NO.:18. In this binding protein the first binding domain may contain the heavy chain variable region of SEQ ID NO: 41 and the light chain variable region of SEQ ID NO:42.

In a still further embodiment the first binding domain may contain (a) a heavy chain CDR1 of SEQ ID NO.:19; (b) a heavy chain CDR2 of SEQ ID NO.:20; (c) a heavy chain CDR3 of SEQ ID NO.:21; (d) a light chain CDR1 of SEQ ID NO.:22; (e) a light chain CDR2 of SEQ ID NO.:23; and (f) a light chain CDR3 of SEQ ID NO.:24. In this binding protein the first binding domain may contain the heavy chain variable region of SEQ ID NO: 43 and the light chain variable region of SEQ ID NO:44.

In yet a further embodiment the first binding domain may contain (a) a heavy chain CDR1 of SEQ ID NO.:25; (b) a heavy chain CDR2 of SEQ ID NO.:26; (c) a heavy chain CDR3 of SEQ ID NO.:27; (d) a light chain CDR1 of SEQ ID NO.:28; (e) a light chain CDR2 of SEQ ID NO.:29; and (f) a light chain CDR3 of SEQ ID NO.:30. In this binding protein the first binding domain may contain the heavy chain variable region of SEQ ID NO: 45 and the light chain variable region of SEQ ID NO:46.

In a further embodiment the first binding domain may contain (a) a heavy chain CDR1 of SEQ ID NO.:31; (b) a heavy chain CDR2 of SEQ ID NO.:32; (c) a heavy chain CDR3 of SEQ ID NO.:33; (d) a light chain CDR1 of SEQ ID NO.:34; (e) a light chain CDR2 of SEQ ID NO.:35; and (f) a light chain CDR3 of SEQ ID NO.:36. In this binding protein the first binding domain may contain the heavy chain variable region of SEQ ID NO: 47 and the light chain variable region of SEQ ID NO:48.

In any of the these binding proteins the second binding domain may contain (a) a heavy chain CDR1 of SEQ ID NO.:49; (b) a heavy chain CDR2 of SEQ ID NO.:50; (c) a heavy chain CDR3 of SEQ ID NO.:51; (d) a light chain CDR1 of SEQ ID NO.:52; (e) a light chain CDR2 of SEQ ID NO.:53; and (f) a light chain CDR3 of SEQ ID NO.:54. In this binding protein the first binding domain may contain the heavy chain variable region of SEQ ID NO: 55 and the light chain variable region of SEQ ID NO:56.

Further provided are binding proteins where the first binding domain is an antibody binding domain that specifically binds and inhibits activation of PD-1 or PD-L1, and where the second binding domain contains an interleukin-1β-binding domain from an interleukin-1 receptor type 1 (IL-1R1) or interleukin-1 receptor type 2 (IL-1R2), optionally coupled to a ligand binding domain from IL-1R accessory protein. For example, such a binding protein may contain a first protein chain containing (a) an interleukin-1β-binding domain of IL-1R1 linked to (b) a VH domain of an immunoglobulin that binds and inhibits PD-1 or PD-L1 linked to (c) an immunoglobulin Fc domain; and a second protein chain containing a VL domain of the immunoglobulin that binds PD-1 or PD-L1. In another example, the binding protein may contain a first protein chain containing (a) a VH domain of an immunoglobulin that binds that binds and inhibits PD-1 or PD-L1 linked to (b) an interleukin-1β-binding domain of IL-1R1 linked to (c) an immunoglobulin Fc domain; and a second protein chain containing a VL domain of the immunoglobulin that binds and inhibits PD-1 or PD-L1. In yet another example, the binding protein may contain two identical protein chains where each protein chain contains (a) an interleukin-1β-binding domain of IL-1R1 linked to (b) an immunoglobulin Fc domain linked to (c) an scFV domain that binds and inhibits activation of PD-1 or PD-L1. In a further example, the binding protein may contain: a first protein chain containing (a) an interleukin-1β-binding domain of IL-1R1 linked to (b) VL and CL domains of an immunoglobulin that binds and inhibits PD-1 or PD-L1 linked to (c) an immunoglobulin Fc domain; and a second protein chain containing VH and CH1 domains of the immunoglobulin that binds and inhibits PD-1 or PD-L1. In still another example, the binding protein may contain: a first protein chain containing (a) VL and CL domains of an immunoglobulin that binds that binds and inhibits PD-1 or PD-L1 linked to (b) an interleukin-1β-binding domain of IL-1R1 linked to (c) an immunoglobulin Fc domain; and a second protein chain containing VH and CH1 domains of the immunoglobulin that binds and inhibits PD-1 or PD-L1.

Nucleic acid molecules that encode the protein chains described above are provided, together with vectors, including expression vectors that contain these nucleic acid molecules.

Methods also are provided for the preparation of a binding protein as described above, where the method includes the steps of a) transforming a host cell with vectors that containing nucleic acid molecules encoding the first binding domains and the second binding domain; b) culturing the host cell under conditions that allow synthesis of the binding protein; and c) recovering the binding protein from the culture. The host cell may contain vectors containing nucleic acid molecules encoding the first binding domain and second binding domain.

Pharmaceutical compositions also are provided that contain a binding protein as described above, together with a pharmaceutically acceptable excipient.

Also provided are bispecific binding proteins (“FAT” binding proteins) that contain a first protein chain, a second protein chain and a third protein chain, where the first protein chain contains a heavy chain having VH, CH1, CH2, and CH3 domains, and a first Fab domain (Fab1) at a solvent exposed loop in the CH2 domain, the CH3 domain, or at the interface of the CH2 and CH3 domains; where the second chain contains a second Fab domain and where the third chain contains a third Fab domain. In these binding proteins the second chain Fab domain associates with the VH and CH1 domains of the first protein chain to form a first binding domain, and the third chain Fab domain associates with the first Fab domain at the solvent exposed loop in the first protein to form a second binding domain. In these binding proteins the solvent exposed loop may contain an amino acid sequence from the CH2 domain, such as ISRTP (SEQ ID NO:57). The solvent exposed loop may contain an amino acid sequence from the CH3 domain, such as SNG. The solvent exposed loop may contain an amino acid sequence from the interface of the CH2 domain and the CH3 domain, such as AKGQP (SEQ ID NO:58). The CH1 domain may be connected to the CH2 domain via an antibody hinge region. The CH2 and CH3 domains may contain an Fc region, such as an Fc region from an IgGl, IgG2, IgG3, IgG4, IgA, IgM, IgE, and IgD. The first protein chain further may contain a first peptide linker between a first terminus of the first Fab domain and the CH2 domain, CH3 domain, or interface of the CH2 and CH3 domains, and/or a second peptide linker between the second terminus of the first Fab domain and the CH2 domain, CH3 domain, or interface of the CH2 and CH3 domains. The first and the second peptide linker may be, for example, (G45)2 (SEQ ID NO:59), (G45)3, (SEQ ID NO:60), and (G45)4 (SEQ ID NO:61). In a first embodiment, the first protein chain may contain the following polypeptide domains, from N-terminus to C-terminus: VH1-CH1-hinge-CH2(N-term)-Fab1-CH2(C-term)-CH3, or in a second embodiment may contain the following polypeptide domains, from N-terminus to C-terminus: VH1-CH1-hinge-CH2-CH3(N-term)-Fab1-CH3(C-term). In a third embodiment the first protein chain may contain the following polypeptide domains, from N-terminus to C-terminus: VH1-CH1-CH2-Fab1-CH3. The first binding domain may bind specifically to PD-1 or PD-L1 and the second binding domain may bind specifically to IL-1β or IL-1R, or the first binding domain may bind specifically to IL-1β or IL-1R and the second binding domain may bind specifically to PD-1 or PD-L1.

In some embodiments of a FAT binding protein the CDR regions of the first binding domain may be selected from the group consisting of the CDR domains of SEQ ID NO:1-6: the CDR domains of SEQ ID NO:7-12; the CDR domains of SEQ ID NO:13-18; the CDR domains of SEQ ID NO:19-24, the CDR domains of SEQ ID NO:25-30; and the CDR domains of SEQ ID NO:31-36 and the CDR regions of the second binding domain may be the CDR domains of SEQ ID NO:49-54.

In further embodiments of the FAT binding proteins the CDR regions of the first binding domain may be the CDR domains of SEQ ID NO:49-54 and the CDR regions of the second binding domain may be selected from the group consisting of: CDR domains of SEQ ID NO:1-6: the CDR domains of SEQ ID NO:7-12; the CDR domains of SEQ ID NO:13-18; the CDR domains of SEQ ID NO:19-24, the CDR domains of SEQ ID NO:25-30; and the CDR domains of SEQ ID NO:31-36.

Nucleic acid molecules that encode the FAT binding protein chains described above are provided, together with vectors, including expression vectors that contain these nucleic acid molecules.

Also provided are pharmaceutical compositions containing one or more FAT binding proteins and a pharmaceutically acceptable carrier.

Methods for the preparation of a FAT binding protein are provided that include the steps of a) transforming a host cell with vectors that may contain nucleic acid molecules encoding the first, second and third protein chains; b) culturing the host cell under conditions that allow synthesis of the binding protein; and c) recovering the FAT binding protein from the culture. The vectors may contain nucleic acid molecules encoding the first, second and protein chains of the FAT protein.

Methods of treating cancer in a subject are provided that include administering a binding protein or pharmaceutical composition as described above to a subject in need thereof. These methods optionally include administering an antitumor agent to the subject in addition to the binding protein.

In these methods of treating cancer, the subject may previously have been treated with cancer immune therapy or have been found to be resistant to the therapy. The subject may have previously been treated with cancer immune therapy or been found to be refractory to cancer immune therapy. The cancer immune therapy may be, for example, treatment with at least one immune checkpoint inhibitor.

The methods of treating cancer may also include administering an additional anti-tumor therapy to the subject, such as chemotherapy, immune therapy, treatment with biologics or small molecules, vaccination, and/or a cell therapy.

Also provided are methods of preventing or reducing the risk of cancer in a subject at risk thereof, that include administering to the subject an effective amount of a binding protein or pharmaceutical composition as described above. The subject may previously have been diagnosed with cancer and be in remission or may previously have been treated for cancer. The subject may be considered to be at risk of cancer due to environmental exposure, tobacco use or exposure, genetic mutation, or a family history of cancer.

In these methods of cancer treatment, the cancer may be lung cancer, such as small cell lung cancer, combined small-cell lung carcinoma, and/or non-small cell lung cancer. The non-small cell lung cancer may be, for example, squamous cell lung carcinoma, large cell lung carcinoma, lung adenocarcinoma, pulmonary pleomorphic carcinoma, lung carcinoid tumor, salivary gland carcinoma, or carcinoma NOS (not otherwise specified). The cancer may be combined small-cell lung carcinoma, extrapulmonary small-cell carcinoma, extrapulmonary small-cell carcinoma localized in the lymph nodes or small-cell carcinoma of the prostate, or may be a cancer with microsatellite instability.

Other objects, features and advantages of the present disclosure will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples are given by way of illustration only, since various changes and modifications within the spirit and scope of the disclosure will become apparent to those skilled in the art from this detailed description.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the chain structure of a BiS2 bispecific antibody.

FIG. 2A shows the chain structure of a BiS3 bispecific antibody.

FIG. 2B shows the chain structure of a binding molecule containing (a) an IL-β binding domain derived from IL-1R1 and IL-1R accessory protein and (b) an antibody binding domain.

FIG. 3A shows the chain structure of a FIT-Ig bispecific antibody.

FIG. 3B-3E show the chain structures of four binding molecule containing (a) an IL-1β binding domain derived from IL-1R1 and IL-1R accessory protein and (b) an antibody binding domain

FIG. 4 shows the chain structure of a FAT-Ig bispecific antibody.

FIG. 5 shows the amino acid sequences of bispecific antibodies that bind IL-1β and PD-1. FIG. 5A shows the amino acid sequence of ITA101; FIG. 5B shows the amino acid sequence of ITA102; FIG. 5C shows the amino acid sequence of ITA103 and ITA104;

FIG. 5D shows the amino acid sequence of ITA201; FIG. 5E shows the amino acid sequence of ITA202; FIG. 5F shows the amino acid sequence of ITA203; FIG. 5G shows the amino acid sequence of ITA204; FIG. 5H shows the amino acid sequence of ITA301; FIG. 5I shows the amino acid sequence of ITA302; FIG. 5J shows the amino acid sequence of ITA303; FIG. 5K shows the amino acid sequence of ITA304; ITA401 shows the amino acid sequence of ITC401, ITC402, ITC 403, ITC404, and ITC 405; FIG. 5L shows the amino acid sequence of ITA402; FIG. 5M shows the amino acid sequence of ITA403; FIG. 5N shows the amino acid sequence of ITA404; FIG. 5O shows the amino acid sequence of ITB101; FIG. 5P shows the amino acid sequence of ITB102; FIG. 5Q shows the amino acid sequence of ITB103; FIG. 5R shows the amino acid sequence of ITB104; FIG. 5S shows the amino acid sequence of ITB105; FIG. 5T shows the amino acid sequence of ITB106; FIG. 5U shows the amino acid sequence of ITB107; FIG. 5V shows the amino acid sequence of ITB108; FIG. 5W shows the amino acid sequence of ITB109; FIG. 5X shows the amino acid sequence of ITE101 ; FIG. 5Y shows the amino acid sequence of ITE102; FIG. 5Z shows the amino acid sequence of ITE201; FIG. 5AA shows the amino acid sequence of ITE202; FIG. 5BB shows the amino acid sequence of ITE301; FIG. 5C shows the amino acid sequence of ITE302; FIG. 5DD shows the amino acid sequence of ITF101; FIG. 5EE shows the amino acid sequence of ITF102; FIG. 5FF shows the amino acid sequence of ITF103; FIG. 5GG shows the amino acid sequence of ITF201; FIG. 5HH shows the amino acid sequence of ITF202; FIG. 5II shows the amino acid sequence of ITF301; FIG. 5JJ shows the amino acid sequence of ITF302; FIG. 5KK shows the amino acid sequence of ITF401; FIG. 5LL shows the amino acid sequence of ITF402; FIG. 5MM shows the amino acid sequence of ITF403.

FIGS. 6A-6C show a table of known antibodies and binding molecules that bind IL-1β, IL-1R, PD-1 or PD-L1.

FIG. 7 shows binding of bispecific antibodies to cell membrane-bound PD-1 and soluble IL-1β simultaneously in a multiple-dose sandwich assay, as detected by flow cytometry. Variable binding affinities of ITA series of bispecific antibodies are demonstrated, and all the binding affinities are substantially higher than control human IgG. FIG. 8 shows binding of bispecific antibodies to cell membrane-bound PD-1 and soluble IL-1β simultaneously in a multiple-dose sandwich assay, as detected by flow cytometry. Variable binding affinities of ITC, ITD and ITE series of bispecific antibodies are demonstrated, and all the binding affinities are substantially higher than control human IgG.

FIGS. 9A-C show binding of bispecific antibodies to cell membrane-bound PD-1 in a multiple-dose sandwich assay, as detected by flow cytometry. Variable binding affinities of ITB and ITF series of bispecific antibodies are demonstrated,and all the binding affinities are substantially higher than control human IgG.

FIGS. 10A and 10B show binding of bispecific antibodies to cell membrane-bound PD-1 and soluble IL-1β simultaneously in a multiple-dose sandwich assay, as detected by flow cytometry. Variable binding affinities of ITB and ITF series of bispecific antibodies are demonstrated. All the binding affinities are substantially higher than control human IgG.

FIG. 11 shows that bispecific antibodies block PD-1 activity in a PD-1/PD-L1 reporter assay. Variable blockade activities are demonstrated for the ITA series of bispecific antibodies. All the blockade activies are substantially higher than control human IgG.

FIGS. 12A and 12B show that bispecific antibodies block IL-1β activity in a IL-1β functional assay. Variable blockade activities are demonstrated of the ITA series of bispecific antibodies. All the blockade activies are substantially higher than control human IgG.

DETAILED DESCRIPTION

Bispecific binding proteins are provided that contain at least one first binding domain that specifically binds an immune checkpoint protein and at least one second binding protein that binds IL-1β. The immune checkpoint protein may be, for example, PD-1, PD-L1, A2AR, B7-H3 (CD276), B7-H4 (VTCN1), BTLA, CTLA-4 (CD152), IDO. KIR, LAG3, NOX2, TIM-3, VISTA, SIGLEC7, (CD328), or SIGLEC9 (CD329). Advantageously, the checkpoint protein is PD-1 or PD-L1.

A binding protein simultaneously binds the checkpoint protein PD-1 or PD-L1 and IL-1β or IL-1R and thereby inhibits binding between PD-1 on CD8 T-cells and PD-L1 on a target cell, such as a tumor cell, and IL-1β activity. Simultaneous inhibition of IL-1β activity and PD-1/PD-L1 binding in this fashion provides for improved methods for cancer treatment. The first and second binding domains advantageously are human antibody variable domains. Novel bispecific binding protein formats also are provided that allow for specific binding of two antigens including, but not limited to, a checkpoint protein and a cytokine such as IL-1β. Methods of using the bispecific binding proteins for treating disease, such as cancer, also are provided.

Binding Domains

The binding domains that may be used in the binding proteins as described herein may be in any format that specifically binds the target protein. For example, for binding IL-1β the ligand binding domain of the interleukin type I or type II receptor may be used, optionally fused to a sequence from the IL-1 receptor accessory protein, as in Rilonacept. Advantageously, however, the binding domains are derived from the variable domains of human immunoglobulin molecules. Specifically, the binding domains may be derived from an antibody that binds a checkpoint protein and an antibody that binds IL-1β or IL-1R. Methods of making fully human antibodies that bind a preselected antigen are well known in the art. For example, human antibodies can be selected from large libraries of antibodies displayed on filamentous phage, and the heavy and light chain variable regions of the selected antibodies identified by methods that are well known. See, for example, Winter et al., Annual Review of Immunology 12:433-455 (1994). The nucleic acids encoding these variable regions are then used in constructing the genes encoding the bispecific binding proteins described herein. Alternatively, antibody variable domains from known antibodies may be used. In particular, human antibodies again IL-1β, PD-1 and PD-L1 have been approved for use in treating a variety of disease states in humans, and the variable regions from these antibodies can be used to construct the bispecific binding proteins described herein. Examples of suitable antibodies are shown below in Tables 1 and 6.

Alternatively, the CDR regions from an antibody with known specificity against IL-1β, IL-1R, PD-1 or PD-L1 can be inserted into known human framework regions using methods of CDR grafting that are well known in the art. See, for example, Williams and Matthews, “Humanising Antibodies by CDR Grafting” in Antibody Engineering (Kontermann and Dübel, Eds.) pp 319-339 (Springer, 2010). These CDR regions may be derived from the CDR regions shown or FIG. 1 or from the CDR regions of the antibodies described in Table 6. The skilled artisan will recognize that other antibodies that specifically bind IL-1β, IL-1R, PD-1 or PD-L1 exist in addition to those described herein, and that the CDR regions of those antibodies may be used in constructing the binding proteins as described herein.

With respect to IL-1β, canakinumab is an FDA-approved human antibody that binds IL-1β, and the amino acid sequences of the heavy and light chain variable regions are well known. See Rondeau et al., MAbs 7:1151 (2015). The entire heavy and light chain variable regions of canakinumab can be used to construct the bispecific protein proteins as described herein; alternatively, the CDR regions of canakinumab can be inserted into alternative human variable framework sequences using methods of CDR grafting that are well known in the art. See, for example, Winter and Harris, Trends in Pharmacological Sciences 14:139-143 (1993). An alternative IL-1β binding antibody is the humanized SK48-E26 antibody described in WO1995/01997.

With respect to IL-1R, anakinra is an FDA-approved, recombinant, nonglycosylated form of human interleukin-1 receptor antagonist (IL-1Ra) Compared to native human IL-1Ra, anakinra contains an extra N-terminal methionine residue. Anakinra competitively inhibits binding of IL-1α and IL-1β to the receptor type 1. This IL-1R1 binding domain can be used in construction of bispecific proteins to block binding of IL-1β to the IL-1 receptor. The sequence of the IL-1R1 binding portion of anakinra, which may be used as a suitable binding domain, is

(SEQ ID NO: 72) MRPSGRKSSKMQAFRIWDVNQKTFYLRNNQLVAGYLQGPNVNLEEKIDVVP IEPHALFLGIHGGKMCLSCVKSGDETRLQLEAVNITDLSENRKQDKRFAFI RSDSGPTTSFESAACPGWFLCTAMEADQPVSLTNMPDEGVMVTKFYFQEDE

With respect to PD-1, pembrolizumab is a humanized antibody that was first approved by the FDA in 2014 and that is used for treatment of a variety of cancers where the tumor cells express elevated PD-1. Nivolumab is a fully human antibody that was first approved by the FDA in 2014 and also is used for treating a variety of cancers. Cemiplimab is a human antibody that was first approved in 2018 for treatment of metastatic cutaneous squamous cell carcinoma. The amino acid sequences for the heavy and light chain variable domains of pembrolizumab, nivolumab, and cemiplimab, are known, as are the sequences of the CDR regions.

With respect to PD-L1, durvalumab is a human antibody that was first approved in 2017 for treatment of metastatic urothelial cancer. Atezolizumab was first approved in 2016 and is used for treating lung cancer. The amino acid sequences for the heavy and light chain variable domains of durvalumab and atezolizumab are known, as are the sequences of the CDR regions.

The sequences of the variable domains and CDR regions of pembrolizumab, nivolumab, cemeplimab, atezolizumab, avelumab, durvalumab and canakinumab are shown in Table 1 below. A list of other known antibodies again IL-1β, PD-1 and PD-L1 is shown in FIG. 6.

TABLE 1 SEQ ID Antibody Domain Sequence NO Pembrolizumab VH CDR1 NYYMY  1 VH CDR2 GINPSNGGTNFNEKFKN  2 VH CDR3 RDYRFDMGFDY  3 VL CDR1 RASKGVSTSGYSYLH  4 VL CDR2 LASYL  5 VL CDR3 QHSRDLPLT  6 VH QVQLVQSGVEVKKPGASVKVSCKASGYTFTNYYM 37 YWVRQAPGQGLEWMGGINPSNGGTNFNEKFKN RVILTTDSSITTAYMELKSLQFDDTAVYYCARRDY RFDMGFDYWGQGTTVTVSS VL EIVLTQSPATLSLSPGERATLSCRASKGVSTSGYSYL 38 HWYQQKPGQAPRLLIYLASYLESGVPARFSGSGSG TDFTLTISSLEPEDFAVYYCQHSRDLPLTFGGGTKVE IK Nivolumab VH CDR1 NSGMH  7 VH CDR2 VIWYDGSKRYYADSVKG  8 VH CDR3 NDDY  9 VL CDR1 RASQSVSSYLA 10 VL CDR2 DASNRAT 11 VL CDR3 QQSSNWPRT 12 VH QVQLVESGGGVVQPGRSLRLDCKASGITFSNSGM 39 HWVRQAPGKGLEWVAVIWYDGSKRYYADSVKGR FTISRDNSKNTLFLQMNSLRAEDTAVYYCATNDDY WGQGTLVTVSS VL s 40 Cemiplimab VH CDR1 GFTFSNFG 13 VH CDR2 ISGGGRDT 14 VH CDR3 VKWGNIYFDY 15 VL CDR1 LSINTF 16 VL CDR2 AAS 17 VL CDR3 QQSSNTPFT 18 VH EVQLLESGGVLVQPGGSLRLSCAASGFTFSNFGMT 41 WVRQAPGKGLEWVSGISGGGRDTYFADSVKGRF TISRDNSKNTLYLQMNSLKGEDTAVYYCVKWGNIY FDYWGQGTLVTVSS VL DIQMTQSPSSLSASVGDSITITCRASLSINTFLNWY 42 QQKPGKAPNLLIYAASSLHGGVPSRFSGSGSGTDF TLTIRTLQPEDFATYYCQQSSNTPFTFGPGTVVDFR SK48-E26 VH CDR1 SYDMS 62 VH CDR2 YISSGGGGTYYPDTVKG 63 VH CDR3 GGVRRGYFDV 64 VL CDR1 RASGNIHNYLT 65 VL CDR2 NAKTLAD 66 VL CDR3 QHFWSIPYT 67 VH EVQLVESGGGVVQPGRSLRLSCSSSGFIFSSYDMS 68 WVRQAPGKGLEWVAYISSGGGGTYYPDTVKGRFT ISRDNSKNTLFLQMDSLRPEDTGVYFCARGGVRRG YFDVWGQGTPVTVSS VL DIQMTQSPSSLSASVGDRVTITCRASGNIHNYLTW 69 YQQTPGKAPKLLIYNAKTLADGVPSRFSGSGSGTD YTFTISSLQPEDIATYYCQHFWSIPYTFGQGTKLQIT Atezolizumab VH CDR1 GFTFSDSWIH 19 VH CDR2 AWISPYGGST 20 VH CDR3 RHWPGGFDY 21 VL CDR1 RASQDVSTAVA 22 VL CDR2 SASFLYS 23 VL CDR3 QQYLYHPAT 24 VH EVQLVESGGGLVQPGGSLRLSCAASGFTFSDSWIH 43 WVRQAPGKGLEWVAWISPYGGSTYYADSVKGRF TISADTSKNTAYLQMNSLRAEDTAVYYCARRHWP GGFDYWGQGTLVTVSS VL DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVA 44 WYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGT DFTLTISSLQPEDFATYYCQQYLYHPATFGQGTKVE IK Avelumab VH CDR1 SYIM 25 VH CDR2 SIYPSGGITFYADTVKG 26 VH CDR3 IKLGTVTTVDY 27 VL CDR1 TGTSSDVGGYNYVS 28 VL CDR2 DVSNRPS 29 VL CDR3 SSYTSSSTRV 30 VH EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYIMM 45 WVRQAPGKGLEWVSSIYPSGGITFYADTVKGRFTI SRDNSKNTLYLQMNSLRAEDTAVYYCARIKLGTVT TVDYWGQGTLVTVSS VL QSALTQPASVSGSPGQSITISCTGTSSDVGGYNYVS 46 WYQQHPGKAPKLMIYDVSNRPSGVSNRFSGSKSG NTASLTISGLQAEDEADYYCSSYTSSSTRVFGTGTK VTVL Durvalumab VH CDR1 RYWMS 31 VH CDR2 NIKQDGSEKYYVDSVKG 32 VH CDR3 EGGWFGELAFDY 33 VL CDR1 RASQRVSSSYLA 34 VL CDR2 DASSRAT 35 VL CDR3 QQYGSLPWT 36 VH EVQLVESGGGLVQPGGSLRLSCAASGFTFSRYWM 47 SWVRQAPGKGLEWVANIKQDGSEKYYVDSVKGR FTISRDNAKNSLYLQMNSLRAEDTAVYYCAREGG WFGELAFDYWGQGTLVTVSS VL EIVLTQSPGTLSLSPGERATLSCRASQRVSSSYLAW 48 YQQKPGQAPRLLIYDASSRATGIPDRFSGSGSGTDF TLTISRLEPEDFAVYYCQQYGSLPWTFGQGTKVEIK Canakinumab VH CDR1 VYGMN 49 VH CDR2 IIWYDGDNQYYADSVKG 50 VH CDR3 DLRTGP 51 VL CDR1 RASQSIGSSLH 52 VL CDR2 ASQSFS 53 VL CDR3 HQSSSLP 54 VH QVQLVESGGGVVQPGRSLRLSCAASGFTFSVYGM 55 NWVRQAPGKGLEWVAIIWYDGDNQYYADSVKG RFTISRDNSKNTLYLQMNGLRAEDTAVYYCARDLR TGPFDYWGQGTLVTVSS VL EIVLTQSPDFQSVTPKEKVTITCRASQSIGSSLHWY 56 QQKPDQSPKLLIKYASQSFSGVPSRFSGSGSGTDFT LTINSLEAEDAAAYYCHQSSSLPFTFGPGTKVDIK

The 1L-1 Receptor type has a binding domain with the sequence:

(SEQ ID NO: 70) KCKEREEKIILVSSANEIDVRPCPLNPNEHKGTITWYKDDSKTPVSTEQAS RIHQHKEKLWFVPAKVEDSGHYYCVVRNSSYCLRIKISAKFVENEPNLCYN AQAIFKQKLPVAGDGGLVCPYMEFFKNENNELPKLQWYKDCKPLLLDNIHF SGVKDRLIVMNVAEKHRGNYTCHASYTYLGKQYPITRVIEFITLEENKPTR PVIVSPANETMEVDLGSQIQLICNVTGQLSDIAYWKWNGSVIDEDDPVLGE DYYSVENPANKRRSTLITVLNISEIESRFYKHPFTCFAKNTHGIDAAYIQL IYPVTN

Rilonacept is an immunoglobulin fusion protein, where the binding domain contains the IL-1 receptor accessory protein (IL-1RAP) fused to the type I IL-1 receptor. The sequence of the IL-1-binding portion of Rilonacept, which may be used as a suitable binding domain, is:

(SEQ ID NO: 71) SERCDDWGLDTMRQIQVFEDEPARIKCPLFEHFLKFNYSTAHSAGLTLIWY WTRQDRDLEEPINFRLPENRISKEKDVLWFRPTLLNDTGNYTCMLRNTTYC SKVAFPLEVVQKDSCFNSPMKLPVHKLYIEYGIQRITCPNVDGYFPSSVKP TITWYMGCYKIQNFNNVIPEGMNLSFLIALISNNGNYTCVVTYPENGRTFH LTRTLTVKVVGSPKNAVPPVIHSPNDHVVYEKEPGEELLIPCTVYFSFLMD SRNEVWWTIDGKKPDDITIDVTINESISHSRTEDETRTQILSIKKVTSEDL KRSYVCHARSAKGEVAKAAKVKQKVPAPRYTVEKCKEREEKIILVSSANEI DVRPCPLNPNEHKGTITWYKDDSKTPVSTEQASRIHQHKEKLWFVPAKVED SGHYYCVVRNSSYCLRIKISAKFVENEPNLCYNAQAIFKQKLPVAGDGGLV CPYMEFFKNENNELPKLQWYKDCKPLLLDNIHFSGVKDRLIVMNVAEKHRG NYTCHASYTYLGKQYPITRVIEFITLEENKPTRPVIVSPANETMEVDLGSQ IQLICNVTGQLSDIAYWKWNGSVIDEDDPVLGEDYYSVENPANKRRSTLIT VLNISEIESRFYKHPFTCFAKNTHGIDAAYIQLIYPVTN

Bispecific Binding Protein Structure

Once the appropriate binding domains are selected, they are incorporated into a format that contains at least one binding domain that specifically binds IL-1β or IL-1R and at least one domain that specifically binds a checkpoint protein. Advantageously, the format of the binding protein is that of a bivalent or multivalent bispecific antibody, containing immunoglobulin variable and constant chain domains arranged to contain two different binding domains, as opposed to the naturally occurring homodimeric structure of a bivalent but monospecific human antibody.

Methods of making bispecific antibodies are well known in the art and are described in, for example, Brinkmann and Kontermann, mAbs 9:182 (2017) and Spiess et al., Molecular Immunology, 67: 95-106 (2015). The bispecific binding proteins described herein can be in any format known in the art that is stable, suitable for administering to a subject, and contains at least one binding domain the binds IL-1β or IL-1R and at least one binding domain that binds a checkpoint protein.

Examples of suitable bispecific binding protein formats known in the art include: Fc-less bispecific antibody formats, including: two scFv molecules joined by a linker (Kontermann, Acta Pharmacol Sin 26:1-9 (2005)); bispecific single-domain antibody fusion proteins (Weidle et al., Cancer Genomics Proteomics 10:155-68 (2013;)) and diabodies (Atwell et al., Mol Immunol 33:1301-12 (1996)); Fab fusion proteins (Schoonjans et al., J Immunol; 165:7050-7 (2000); and miniantibodies (Pluckthun and Pack, Immunotechnology 3:83-105 (1997) and Muller et al., FEBS Lett 432:45 49(1998));

Asymmetric IgGs with heavy and light chains from two different antibodies (Suresh et al, Methods Enzymol; 121:210-28 (1986)); and

Bispecific IgGs with an asymmetric Fc region, e.g. asymmetric Fc regions using the “knobs into holes” method (Ridgway et al., Protein Eng; 9:617-21 (1996); Shatz et al., MAbs; 5:872-81 (2013)); Sampei et al., PLoS One; 8:e57479 (2013); Spiess et al., Biotechnol; 31:753-8 (20130; Juntilla et al., Cancer Res. 74:5561-71 (2014); and Sun et al., J Clin Invest. 125):4077-4090 (2015)).

The skilled artisan will recognize that a large number of bispecific antibody formats in addition to the specific formats described above can be used to construct a bispecific antibody that binds IL-1β or IL-1R and a checkpoint protein. Advantageously, the bispecific antibody is either a 2+2 scFv-based structure or a 2+2 Fab-based structure as described in more detail below.

2+2 scFv-Based Structures

A first 2+2 scFv-based structure is the structure shown in FIG. 1, referred to herein as BiS2. As shown in FIG. 1, the BiS2 format contains two protein chains:

(1) a heavy chain that contains (from N- to C-terminus): a single chain Fv containing a first VH domain and a first VL domain (arranged VH-VL or VL-VH, i.e. the domains can be in either order), where the scFv binds the first target (IL-1β, IL-1R or the checkpoint protein, respectively); a second VH domain; and CH1, CH2, and CH3 domains, and (2) a light chain that contains (from N- to C-terminus): a second VL domain and a CL domain.

The BiS2 protein assembles via non-covalent homodimeric binding of the CH3 and CH2 domains and heterodimeric binding between the CH1 and CL domains on the heavy chain and the second VH and VL domains on the light chain. The binding between the CH1 and CL domains and the VH and VL domains forms a Fab domain that binds the second target (the checkpoint protein or IL-1 β/IL-1R, respectively). Advantageously, disulfide bonds also form between the hinge regions, and between the CH1 and CL domains in the same manner as are found in naturally-occurring IgG molecules.

A second 2+2 sc Fv-based structure is the structure shown in FIG. 2A, referred to herein as BiS3. As shown in FIG. 2A, the BiS3 format also contains two protein chains:

(1) a heavy chain that contains (from N- to C-terminus): a first VH domain; CH1, CH2, and CH3 domains; and a single chain Fv containing a second VH domain and a second VL domain (where the VH and VL domains can be in either order), where the scFv binds the first target (IL-1β or the checkpoint protein, respectively);

(2) a light chain that contains (from N- to C-terminus): a second VL domain and a CL domain.

The BiS3 protein also assembles via homodimeric binding of the CH3 and CH2 domains and heterodimeric binding between the CH1 and CL domains on the heavy chain and the second VH and VL domains on the light chain. The binding between the CH1 and

CL domains and the VH and VL domains forms a Fab domain that binds the second target (the checkpoint protein or IL-1β/IL-1R, respectively). Advantageously, disulfide bonds also form between the CH2 domains, and between the CH1 and CL domains in the same manner as are found in naturally-occurring IgG molecules.

An alternative binding protein structure is the homodimeric structure shown in FIG. 2B, in which the heavy chain VH and CH1 domains are replaced by a binding domain derived from the extracellular ligand binding domain of an interleukin-1 receptor. This binding domain contains all or part of the extracellular binding domain from type 1 or type 2 IL-1R, optionally conjugated to the extracellular protein binding domain from interleukin-1 accessory protein (IL-1RAcP). IL-1RAcP is a receptor subunit of the functional IL-1 receptor and forms a receptor heterodimer with IL-1RI. In the structure shown in FIG. 2B the binding protein assembles via non-covalent homodimeric binding of the CH3 and CH2 domains. Advantageously, disulfide bonds also form between the CH2 domains, and between the hinge domains in the same manner as are found in naturally-occurring IgG molecules.

2+2 Fab-Based Structures

A first 2+2 Fab-based structure is the structure shown in FIG. 3A, referred to herein as FIT-Ig (see Gong et al., MABS, 2017, 9:1118-1128 (2017)). As shown in FIG. 3A, the FIT-Ig format contains three protein chains:

(1) a heavy chain that contains (from N- to C-terminus): a first VL domain; a first CL domain, a first VH domain, a first CH1 domain, and CH2 and CH3 domains;

(2) a light chain that contains (from N- to C-terminus): a second VL domain and a second CL domain; and

(3) an Fd chain that contains (from N- to C-terminus): a second VH domain and second CH1 domain.

In the heavy chain the first CL domain may be linked to the first VH domain via a peptide linker such as, for example, a flexible hydrophilic linker having the sequence (GGGGS)_(x), where xis 1-5 (SEQ ID NO:123). Advantageously, however, the linker is absent.

The FIT-Ig protein assembles via: non-covalent homodimeric binding of the CH3 and CH2 domains; heterodimeric binding between the first VH and CH1 domains on the heavy chain and the second VL and CL domains on the light chain; and heterodimeric binding between the first VL and CL domains and the second VH and CH1 domains on the Fd chain

Two identical Fab binding domains are formed by binding of the heavy chain to the light chain, and two distinct but identical Fab domains are formed by binding of the heavy chain to the Fd chain as shown in FIG. 3. Advantageously, disulfide bonds also form between the CH2 domains, and between the hinge domains in the same manner as are found in naturally-occurring IgG molecules.

An alternative 2+2 binding protein is shown in FIGS. 3B-3E, in which one of the antibody Fab binding domains is replaced by a binding domain derived from the extracellular ligand binding domain of an interleukin-1 receptor. This binding domain contains all or part of the extracellular binding domain from type 1 or type 2 IL-1R, optionally conjugated to the extracellular protein binding domain from interleukin-1 accessory protein (IL-1RAcP). IL-1RAcP is a receptor subunit of the functional IL-1 receptor and forms a receptor heterodimer with IL-1RI. In the structures shown in FIGS. 3B-E the binding proteins assemble via non-covalent homodimeric binding of the CH3 and CH2 domains; heterodimeric binding between the VH and CH1 domains on one chain and the VL and CL domains on the second protein chain. Advantageously, disulfide bonds also form between: the CH1 and CL domains, between the CH2 domains, and between the hinge domains in the same manner as are found in naturally-occurring IgG molecules.

A second 2+2 Fab-based structure is the novel structure shown in FIG. 4, referred to herein as FAT-Ig. As shown in FIG. 4, the FAT-Ig format contains three protein chains:

(1) a heavy chain that contains (from N- to C-terminus): a first VH domain; a first CH1 domain, and CH2 and CH3 domains; plus first VL and a first CL domain, where the first VL and first CL domains are disposed at a solvent exposed loop in the CH2 domain, the CH3 domain, or at the interface of the CH2 and CH3 domains. Advantageously, the first CL and first CL domains are disposed at a solvent-exposed loop in the CH3 domain.

(2) a light chain that contains (from N- to C-terminus): a second VL domain and a second CL domain; and

(3) an Fd chain that contains (from N- to C-terminus): a second VH domain and second CH1 domain.

In the heavy chain, the first VL and CL disposed at the solvent-exposed loop are connected to the CH2 domain, CH3 domain, or interface of the CH2 and CH3 domains via flexible peptide linkers. The linkers can have 4-25 amino acids and advantageously comprise (GGGGS)_(x) units, where x=1-5 (SEQ ID NO:123). Other linkers may also be used, as described in more detail below.

The FAT-Ig protein assembles as shown in FIG. 4 via: non-covalent homodimeric binding of the CH3 and CH2 domains; heterodimeric binding of the heavy chain CH1 and VH domains with the light chain CL and VL domains; and heterodimeric binding of the heavy chain CL and VL domains with the Fd chain CH1 and VH domains. Two identical Fab binding domains are formed by binding of the heavy chain to the light chain, and two distinct but identical Fab domains are formed by binding of the heavy chain to the Fd chain as shown in FIG. 4. Advantageously, disulfide bonds also form between the hinge domains, and between the CH1 and CL domains in the same manner as are found in naturally-occurring IgG molecules. One of ordinary skill in the art will recognize that the novel FAT-Ig antibody format can be used to bind any two desired antigens, and is not limited to IL-1β/IL-1R and a checkpoint protein.

In each of the four specific binding proteins described above the binding domains that specifically bind IL-1β/IL-1R and the checkpoint protein are disposed asymmetrically within the binding protein i.e. the structure of the binding protein is different when the first binding domain binds IL-1β/IL-1R and the second binding domain binds the checkpoint protein compared to when the first binding domain binds the checkpoint protein and the second binding domain binds IL-1β/IL-1R. Accordingly, each of the four specific binding proteins can exist in two alternative forms for any given pair of binding domains.

Polypeptide Linkers

The domains of the bispecific binding proteins described herein may be joined into contiguous protein chains using linkers. The linkers may be used, for example, to connect the variable heavy and light chains of an scFv, or to connect the CL/VL domains into the heavy chain constant domains in the FAT-Ig format.

Suitable linkers are well known in the art and, when present, advantageously contain at least four amino acids, although longer or shorter linkers may also be used. The linkers advantageously are flexible, hydrophilic and have little or no secondary structure of their own. Linkers may be approximately 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, or approximately 50 residues in length. When multiple linkers are used to interconnect portions of a bispecific protein as described herein, the linkers may be the same, or have different lengths and/or amino acid sequences.

The linker(s) facilitate formation of the desired bispecific binding protein structure. Linkers may contain (Gly-Ser)_(x) units, where x=1-5. Glutamic acid or lysine residues may also be placed in the linker sequences to increase solubility if necessary. The length of the linker may be varied to facilitate protein folding, target binding, and/or expression. For example, different multiples of (Gly-Ser)_(x) units may be used to improve or optimize protein folding, target binding, and/or expression using methods that are well-known in the art.

Preparation of Bispecific Binding Proteins

Methods of making bispecific binding proteins such as Fc-less bispecific antibodies, asymmetric IgGs with heavy and light chains from two different antibodies and bispecific IgGs with an asymmetric Fc region, are well known in the art and are described in the references provided above.

The particular 2+2 bispecific antibodies described above may each be produced using suitable expression constructs in recombinant host cells. Nucleic acids encoding the heavy, light and Fd chains can be prepared synthetically using, for example, a commercial gene synthesis vendor such as Thermo Fisher (Carlsbad, Calif.). Advantageously the host cells are eukaryotic cells and the gene for each chain advantageously is synthesized with a sequence that encodes an N-terminal signal sequence that causes secretion of the translated protein from the host cell. The gene for each chain is inserted into a suitable expression vector, for example, pTT5 vector (Durocher et al., Nucleic Acids Res. 30:E9 (2002)), and the resulting expression constructs are then transfected into a culture of suitable host cells for transient expression. Methods of efficiently transfecting expression vectors into host cells are well known in the art using, for example, cationic lipids. See Felgner et al., Proc. Nat'l Acad. Sci USA 84:7413 (1987). Other methods of delivering expression vectors into cells also are well known in the art. Methods of making host cells that provide stable expression of a desired protein by integrating expression constructs into the genome of suitable host cells also are well known, as are methods of stable expression using episomal vectors containing a mammalian origin of replication that act as extrachromosomal elements in the nucleus of the host cell.

The host cells advantageously are eukaryotic cells, for example, a single-celled eukaryote (e.g., a yeast or other fungus), a plant cell (e.g., a tobacco or tomato plant cell), an animal cell (e.g., a human cell, a monkey cell, a hamster cell, a rat cell, a mouse cell, or an insect cell) or a hybridoma. Examples of host cells include the COS-7 line of monkey kidney cells (ATCC CRL 1651) (see Gluzman et al., 1981, Cell 23:175), L cells, C127 cells, 3T3 cells (ATCC CCL 163), Chinese hamster ovary (CHO) cells or their derivatives such as Veggie CHO and related cell lines which grow in serum-free media (see Rasmussen et al., 1998, Cytotechnology 28:31) or CHO strain DX-B11, which is deficient in DHFR (see Urlaub et al., 1980, Proc. Natl. Acad. Sci. USA 77:4216-20), HeLa cells, BHK (ATCC CRL 10) cell lines, the CV1/EBNA cell line derived from the African green monkey kidney cell line CV1 (ATCC CCL 70) (see McMahan et al., 1991, EMBO J. 10:2821), human embryonic kidney cells such as 293, 293 EBNA or MSR 293, human epidermal A431 cells, human Colo205 cells, other transformed primate cell lines, normal diploid cells, cell strains derived from in vitro culture of primary tissue, primary explants, HL-60, U937, HaK or Jurkat cells. Advantageously, the host cell is a CHO cell, such as CHO-3E7.

Typically, a host cell is a cultured cell that can be transformed or transfected with a polypeptide-encoding nucleic acid, which can then be expressed in the host cell. The phrase “recombinant host cell” can be used to denote a host cell that has been transformed or transfected with a nucleic acid to be expressed. A host cell also can be a cell that comprises the nucleic acid but does not express it at a desired level unless a regulatory sequence is introduced into the host cell such that it becomes operably linked with the nucleic acid. The term “host cell” as used herein refers not only to the particular subject cell but to the progeny or potential progeny of such a cell. Because certain modifications may occur in succeeding generations due to, e.g., mutation or environmental influence, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein. Suitable cell culture media for growing eukaryotic host cells are well known in the art and are commercially available from, for example, Thermo Fisher (Grand Island, NY).

The host cells are cultured under suitable conditions to allow assembly of the protein chains in the endoplasmic reticulum of the host cell, followed by secretion of the bispecific binding proteins into the cell culture supernatant. The assembly of the correct structure of the binding protein (as opposed to, for example, non-specific pairing of the chains leading to formation of inactive proteins) can be improved by altering the relative ratios of the expression vectors used to transfect the host cells. This variation in the vector ratio also can be used to counteract, say, less efficient production of one of the chains compared to a different chain. One skilled in the art will recognize that methods of optimizing the vector ratio(s) are well known in the art.

After the host cells are cultured in an appropriate expression medium for a suitable length of time, the conditioned medium containing the bispecific binding protein is collected, and the bispecific binding protein is purified using methods that are well known in the art. For example, the binding protein can be purified using methods that may include ion-exchange chromatography, size-exclusion chromatography, and affinity chromatography, such as protein A affinity chromatography. Methods of protein purification are described in, for example, Burgess and Deutscher (Eds) “Guide to Protein Purification, Volume 436 (Methods in Enzymology) 2nd Edition (2009). Purity of the protein can be confirmed using methods well-known in the art, such as RT-HPLC, SDS-PAGE and the like.

The correct assembly of the multichain binding protein can be shown by, for example, non-denaturing gel electrophoresis, to show that the binding protein has the expected molecular weight. SDS-PAGE can be used to show that each of the expected protein chains is present and has the expected molecular weight. Western blotting using a suitable anti-Human IgG antibody can further show that the measured proteins are immunoglobulin chains.

Pharmaceutical Compositions and Methods of Administration

Methods of preparing and administering the bispecific binding molecules to a subject in need thereof are well known to or are readily determined by those skilled in the art. The route of administration of the binding molecule can be, for example, oral, parenteral, by inhalation or topical. The term parenteral as used herein includes, for example, intravenous, intraarterial, intraperitoneal, intramuscular, subcutaneous, rectal, or vaginal administration. However, in other methods compatible with the teachings herein, the binding molecules may be delivered directly to the site of the adverse cellular population thereby increasing the exposure of the diseased tissue to the therapeutic agent.

The binding molecules may be administered in a pharmaceutically effective amount for the treatment of diseases such as certain types of cancers. The pharmaceutical compositions can comprise pharmaceutically acceptable carriers, including, for example, water, ion exchangers, proteins, buffer substances, and salts. Preservatives and other additives can also be present. The carrier can be a solvent or dispersion medium. Suitable formulations for use in the therapeutic methods disclosed herein are described in Remington's Pharmaceutical Sciences (Mack Publishing Co.) 16th ed. (1980).

In any case, sterile injectable solutions can be prepared by incorporating the binding molecule(s) by itself or in combination with other active agents in an effective amount in an appropriate solvent followed by filtered sterilization. The preparations may also be packaged and sold in the form of a kit. Such articles of manufacture can have labels or package inserts indicating that the associated compositions are useful for treating a subject suffering from, or predisposed to a disease or disorder.

Parenteral formulations can be a single bolus dose, an infusion or a loading bolus dose followed with a maintenance dose. These compositions can be administered at specific fixed or variable intervals, for example, once a week or monthly, or on an “as needed” basis.

The composition can be administered as a single dose, multiple doses or over an established period of time in an infusion. Dosage regimens also can be adjusted to provide the optimum desired response (for example, a therapeutic or prophylactic response). The composition may be used for treatment of cell-mediated diseases such as certain types of cancers including for example, bone cancer, pancreatic cancer, cancer of the head and neck, cutaneous or intraocular melanoma, uterine cancer, cancer of the central nervous system (CNS), ovarian cancer, rectal cancer, cancer of the anal region, stomach cancer, colon cancer, breast cancer, melanoma, colorectal cancer, testicular cancer, Hodgkin's disease, cancer of the esophagus, cancer of the small intestine, cancer of the endocrine system, sarcomas of soft tissues, cancer of the urethra, cancer of the penis, prostate cancer, chronic or acute leukemia, solid tumors of childhood, lymphocytic lymphomas, cancer of the bladder, cancer of the kidney or ureter, adrenocortical carcinoma, AIDS-related cancers, Childhood Cerebellar Astrocytoma, Childhood Cerebral Astrocytoma, Basal Cell Carcinoma, extrahepatic bile duct cancer, osteosarcoma/malignant fibrous histiocytoma bone cancer, brain tumors, bronchial adenomas/carcinoids, carcinoid tumor, gastrointestinal carcinoid tumor, cerebellar astrocytoma, cerebral astrocytoma/malignant glioma, cervical cancer, childhood cancers, CMML, Chronic Lymphocytic Leukemia, Chronic Myelogenous Leukemia, Chronic Myeloproliferative Disorders, ependymoma, Ewing's Family of Tumors, extracranial germ cell tumor, extragonadal germ cell tumor, extrahepatic bile duct cancer, gallbladder cancer, gastrointestinal carcinoid tumor, germ cell tumors, gestational trophoblastic tumor, glioma, hairy cell leukemia, hepatocellular cancer, hypopharyngeal cancer, hypothalamic and visual pathway glioma, islet cell carcinoma, Kaposi's Sarcoma, laryngeal cancer, leukemia, lip and oral cavity cancer, non-small cell lung cancer (including squamous cell lung carcinoma, large cell lung carcinoma, lung adenocarcinoma, pulmonary pleomorphic carcinoma, lung carcinoid tumor, salivary gland carcinoma), small cell lung cancer (including combined small-cell carcinoma), “not otherwise specified” (NOS) lung cancer, extrapulmonary small-cell carcinoma (including extrapulmonary small-cell carcinoma localized in the lymph nodes and small-cell carcinoma of the prostate), lymphoma, Waldenstrom's Macroglobulinemia, medulloblastoma, mesothelioma, metastatic squamous neck cancer with occult primary, multiple endocrine neoplasia syndrome, multiple myeloma/plasma cell neoplasm, mycosis fungoides, myelodysplastic syndromes, myelodysplastic/myeloproliferative diseases, nasal cavity and paranasal sinus cancer, nasopharyngeal cancer, neuroblastoma, oral cancer, oropharyngeal cancer, ovarian epithelial cancer, ovarian germ cell tumor, ovarian low malignant potential tumor, islet cell pancreatic cancer, parathyroid cancer, pheochromocytoma, pineoblastoma, pituitary tumor, pleuropulmonary blastoma, ureter transitional cell cancer, retinoblastoma, rhabdomyosarcoma, salivary gland cancer, Sezary Syndrome, skin cancer, non-melanoma skin cancer, Merkel Cell Skin Carcinoma, squamous cell carcinoma, testicular cancer, thymoma, gestational trophoblastic tumor, Wilms' Tumor, and cancers with microsatellite instability.

With respect to esophageal cancer, the cancer may be, for example, esophageal squamous-cell carcinomas (ESCC) or esophageal adenocarcinomas (EAC). With respect to pancreatic cancer, the cancer may be, for example, exocrine cancer, pancreatic adenocarcinoma, pancreatic ductal carcinoma, acinar cell carcinoma of the pancreas, cystadenocarcinoma, pancreatoblastoma, adenosquamous carcinomas, undifferentiated carcinomas, pancreatic mucinous cystic neoplasms, neuroendocrine, or pancreatic neuroendocrine tumors (PanNETs). With respect to hepatic cancer, the cancer may be, for example, hepatocellular carcinoma (HCC), hepatoblastoma, cholangiocarcinoma, cholangiocellular cystadenocarcinoma, angiosarcoma, or leiomyosarcoma. With respect to colorectal cancer the cancer may be adenocarcinoma, carcinoid tumors, gastrointestinal stromal tumors (GIST), lymphoma, sarcomas, adenosquamous carcinoma (Ad-SCC) or squamous carcinoma (SCC). With respect to breast cancer, the cancer may be In situ, ductal carcinoma in situ (DCIS), invasive, invasive ductal carcinoma (IDC), invasive lobular carcinoma (ILC), triple-negative breast cancer, inflammatory breast cancer, angiosarcoma, or Paget disease of the breast. With respect to ovarian cancer, the cancer may be epithelial tumors, benign epithelial ovarian tumors, borderline epithelial ovarian tumors, malignant epithelial ovarian tumors, germ cell tumors, teratoma, dysgerminoma, endodermal sinus tumor and choriocarcinoma, primary peritoneal carcinoma, fallopian tube cancer or ovarian stromal tumors. With respect to multiple myeloma & precancerous conditions, the cancer may be light chain myeloma, non-secretory myeloma, solitary plasmacytoma, extramedullary plasmacytoma, monoclonal gammopathy of undetermined significance (MGUS), smoldering multiple myeloma (SMM), Immunoglobulin D (IgD) myeloma or Immunoglobulin E (IgE) myeloma.

Therapeutically effective doses of the compositions for treating these diseases vary depending upon many different factors, including means of administration, target site, physiological state of the patient, whether the patient is human or an animal, other medications administered, and whether treatment is prophylactic or therapeutic. Usually, the patient is a human, but non-human mammals including transgenic mammals can also be treated. Treatment dosages can be titrated using routine methods known to those of skill in the art to optimize safety and efficacy.

The amount of at least one binding molecule to be administered can be readily determined by one of ordinary skill in the art without undue experimentation. Factors influencing the mode of administration and the respective amount of at least one binding molecule include, but are not limited to, the severity of the disease, the history of the disease, and the age, height, weight, health, and physical condition of the individual undergoing therapy. Similarly, the amount of binding molecule, to be administered will depend upon the mode of administration and whether the subject will undergo a single dose or multiple doses of this agent.

The binding molecule, may also be used in the manufacture of a medicament for treating a type of cancer, including, for example, the cancers listed above.

The subject treated with the compositions described herein may be treatment naive or may be pretreated with one or more other therapies (for example, at least one other anti-cancer therapy) prior to receiving the medicament comprising the binding molecule. It is not necessary that the subject was a responder to pretreatment with the prior therapy or therapies. Thus, the subject that receives the medicament comprising the binding molecule, could have responded, responded poorly, responded initially but subsequently failed to respond, or could have failed to respond to pretreatment with the prior therapy, or to one or more of the prior therapies where pretreatment comprised multiple therapies. Accordingly, the present disclosure provides methods to treat patients that are poor responders or non-responders to other therapies comprising administering a binding molecule as described herein. Also provided are methods to overcome or prevent resistance to cancer therapies or to prevent or delay relapse, comprising administering a binding molecule as disclosed herein, or a composition as described herein.

Even if a patient has been previously treated with an anti-cancer medicament, a person skilled in the art can determine whether a person showed no response or was refractory to that medicament. For example, a non-response to an anti-cancer medicament may be reflected in an increased suffering from cancer, such as an increased growth of a cancer/tumor and/or increase in the size of a tumor, in the formation of (or increase in) metastases or an increase in the number or size of metastases. A non-response may also be the development of a tumor or metastases, for example after resection of a tumor, in the shortening of time to disease progression, or in the increase in the size of (a) tumor(s) and/or (a) metastases, for example in neoadjuvant therapy. Based on these parameters or other parameters known in the art, a patient group can be identified that does not respond to treatment with anti-cancer medicaments and this group of patients may then be treated with the binding molecules described herein.

The binding molecules and compositions containing the binding molecules may also be used to treat patients that are, for example, poor-responders or non-responders to another therapy. The term “non-responder” as used herein can refer to an individual/patient/subject that is less likely to respond to a treatment using an anti-cancer medicament. “Less likely to respond” as used herein refers to a decreased likeliness that a pathological complete response will occur in a patient treated with an anti-cancer medicament. In some aspects, a patient can be initially a good responder, and resistance to treatment can develop during treatment with such an anti-cancer medicament, leading to poor or no-response to the treatment.

The term “good responder” as used herein refers to an individual whose tumor does not demonstrate growth, metastases, increase in number or size of metastases, etc. during or after treatment using an anti-cancer medicament, for example based on serial imaging studies, an individual that does not experience tumor growth, metastases, increase in number or size of metastases, etc. over a period of time (for example, about 1 year following initial diagnosis), and/or an individual that experiences a certain life span (for example, about 2 years or more following initial diagnosis).

The term “poor responder” as used herein refers to an individual whose tumor grows or metastasizes during or shortly thereafter standard therapy, for example using an anti-cancer medicament, or who experiences adverse clinical effects attributable to the tumor. The term “poor responder” also includes indivduals who transitioned from “good responder” to ‘poor responder” during treatment with an anti-cancer medicament.

In cases where it is assessed that the subject is a “non-responder,” a “poor-responder” or is “less likely to respond” (based, for example, on the presence of certain biomarkers in the cancer cells), the subject could be treated with the binding molecules disclosed herein.

Methods also are provided for the co-administration of a binding molecule as described herein and at least one other therapy. The binding molecule and the at least one other therapy can be co-administered together in a single composition or can be co-administered together at the same time or overlapping times in separate compositions. In some aspects, a binding molecule can be used as an adjuvant therapy.

The binding molecule may also be used in the manufacture of a medicament for treating a subject suffering from a cancer, where the binding molecule is administered before a subject has been treated with at least one other therapy.

The binding molecules can also be used in methods of preventing or reducing the risk of cancer in a subject by administering to the subject an effective amount of a binding protein or composition containing the binding protein. The cancer may be lung cancer and the patient may be in remission from a previously diagnosed and/or previously treated cancer. The patient may be considered to be at risk of cancer due to environmental exposure, tobacco use or exposure, genetic mutation, or a family history of cancer.

EXAMPLES

In the examples below the binding domains are based on heavy and light chain variable regions from human antibodies that have received regulatory approval for use in humans. “O,” “E” and “K” indicate domains that bind IL-1β, while “M” and “B” indicate binding domains that bind PD-1. The amino acid sequences of the chains of the binding proteins are shown in FIG. 5

Example 1 Expression of Bispecific Antibodies

1. Plasmid Preparation

Target DNA sequences encoding the binding proteins were synthesized and subcloned into the pTT5 vector (Durocher et al., Nucleic Acids Res. 30:E9 (2002) for expression in CHO-3E7 cells. The amino acid sequences of the coding sequences are shown in FIG. 5.

2. Cell Culture and Transient Transfection

CHO-3E7 cells were grown in serum-free FreeStyle™ CHO Expression Medium (Life Technologies, Carlsbad, Calif., USA). The cells were maintained in Erlenmeyer Flasks (Corning Inc., Acton, Mass.) at 37° C. with 5% CO₂ on an orbital shaker (VWR Scientific, Chester, Pa.). One day before transfection, the cells were seeded in Corning Erlenmeyer Flasks. On the day of transfection, DNA and transfection reagent were mixed and then added into the cells culture, during which the recombinant plasmids encoding target antibody were transiently transfected into CHO-3E7 cells. The cell culture supernatant collected on day 6 was used for purification. Table 2 lists the heavy chain, light chain and Fd chain combination of each antibody and each of the plasmid ratios that were screened.

TABLE 2 Summary of heavy chain (HC), light chain (LC) and Fd chain (Fd) combinations and plasmid ratios for each antibody. Antibody Antibody Ratio 1 Ratio 2 Ratio 3 Ratio 4 name format HC name LC name Fd HC:LC:Fd HC:LC:Fd HC:LC:Fd HC:LC:Fd ITA101 BiS2-OB BscFv-OHC OLC / 1:1:0 3:1:0 1:3:0 / ITA102 BiS2-OM MscFv-OHC OLC / 1:1:0 3:1:0 1:3:0 / ITA103 BiS2-PC OscFv-BHC BLC / 1:1:0 3:1:0 1:3:0 / ITA104 BiS2-MO OscFv-MHC MLC / 1:1:0 3:1:0 1:3:0 / ITA201 BiS3-OB OHC-BscFv OLC / 1:1:0 3:1:0 1:3:0 / ITA202 BiS3-OM OHC-MscFv OLC / 1:1:0 3:1:0 1:3:0 / ITA203 BiS3-BO BHC-OscFv BLC / 1:1:0 3:1:0 1:3:0 / ITA204 BiS3-MO MHC-OscFv MLC / 1:1:0 3:1:0 1:3:0 / ITA301 FiT-OB BLC-OHC OLC BFd 1:1:1 1:3:3 1:1:3 1:3:1 ITA302 FiT-OM MLC-OHC OLC MFd 1:1:1 1:3:3 1:1:3 1:3:1 ITA303 FiT-BO OLC-BHC BLC OFd 1:1:1 1:3:3 1:1:3 1:3:1 ITA304 FiT-MO OLC-MHC MLC OFd 1:1:1 1:3:3 1:1:3 1:3:1 ITA401 FAT-OB OHC-BLC OLC BFd 1:1:1 1:3:3 1:1:3 1:3:1 ITA402 FAT-OM OHC-MLC OLC MFd 1:1:1 1:3:3 1:1:3 1:3:1 ITA403 FAT-BO BHC-OLC BLC OFd 1:1:1 1:3:3 1:1:3 1:3:1 ITA404 FAT-MO MHC-OLC MLC OFd 1:1:1 1:3:3 1:1:3 1:3:1 ITB101 FP2-BK K BHC B LC / 1:1 ITB102 FP2-MK K MHC M LC / 1:1 ITB103 FFP1(FIT)- KM MFd-K-G4P M LC / 1:1 ITB104 FFP1(FIT)-KB BFd-K-G4P B LC / 1:1 ITB105 FFP3-KM K-G4P-MscFv / / N/A ITB106 FP1- K-BLC-Fc / B Fd 1:1 (crossmab)BK ITB107 FP1- K-MLC-Fc / M Fd 1:1 (crossmab) MK ITB108 FFP2-KM MLC-KG4P / M Fd 1:1 ITB109 FFP2-KB BLC-K-G4P / B Fd 1:1 ITC401 FAT-O/B 1 + 5 O HC-B LC 1 + 5 O LC B Fd 1:1:1 1:3:3 1:1:3 1:3:1 ITC402 FAT-O/B 3 + 3 O HC-B LC 3 + 3 O LC B Fd 1:1:1 1:3:3 1:1:3 1:3:1 ITC403 FAT-O/B 4 + 2 O HC-B LC 4 + 2 O LC B Fd 1:1:1 1:3:3 1:1:3 1:3:1 ITC404 FAT-O/B 5 + 1 O HC-B LC 5 + 1 O LC B Fd 1:1:1 1:3:3 1:1:3 1:3:1 ITC405 FAT-O/B 4 + 4 O HC-B LC 4 + 4 O LC B Fd 1:1:1 1:3:3 1:1:3 1:3:1 ITC406 FAT-O/B 2 + 2 O HC-B LC 2 + 2 O LC B Fd 1:1:1 1:3:3 1:1:3 1:3:1 ITD401 FAT-O/B 5 + 5 FAT-O/B 5 + 5 O LC B Fd 1:1:1 1:3:3 1:1:3 1:3:1 ITD402 FAT-O/B 4 + 5 FAT-O/B 4 + 5 O LC B Fd 1:1:1 1:3:3 1:1:3 1:3:1 ITD403 FAT-O/B 5 + 4 FAT-O/B 5 + 4 O LC B Fd 1:1:1 1:3:3 1:1:3 1:3:1 ITE101 BiS2-O/M VH/VL DSB M scFv-O HC VH/VL DSB O LC / 1:1:0 3:1:0 1:3:0 / ITE102 BiS2-O/M VL/VH DSB M scFv-O HC VL/VH DSB O LC / 1:1:0 3:1:0 1:3:0 / ITE201 BiS3-M/O VH/VL DSB M HC-O scFv_VH/VL DSB M LC / 1:1:0 3:1:0 1:3:0 ITE202 BiS3-M/O VL/VH DSB M HC-O scFv_VL/VH DSB M LC / 1:1:0 3:1:0 1:3:0 ITE301 FIT-B/O-L3 O LC-B HC-L3 B LC O Fd 1:1:1 1:3:3 1:1:3 1:3:1 ITE302 FIT-B/O-L7 O LC-B HC-L7 B LC O Fd 1:1:1 1:3:3 1:1:3 1:3:1 ITF101 BiS2-E/M VL/VH DSB BiS2-E/M VL/VH DSB E13 LC / 1:1:0, 1:3:0 3:1:0 ITF102 BiS2-M/E VL/VH DSB BiS2-M/E VL/VH DSB M LC / 1:1:0, 1:3:0 3:1:0 ITF103 BiS2-M/E VH/VL DSB BiS2-M/E VH/VL DSB M LC / 1:1:0, 1:3:0 3:1:0 ITF201 BiS3-M/E VL/VH DSB BiS3-M/E VL/VH DSB M LC / 1:1:0, 1:3:0 3:1:0 ITF202 BiS3-M/E VH/VL DSB BiS3-M/E VH/VL DSB M LC / 1:1:0, 1:3:0 3:1:0 ITF301 FIT-B/E L3 FIT-B/E-L3 B LC E Fd 1:1:1 1:1:1, 1:1:1, 1:1:1, ITF302 FIT-B/E L7 FIT-B/E-L7 B LC E Fd 1:1:1 1:1:1, 1:1:1, 1:1:1, ITF401 FAT-E/B FAT-E/B E13LC B Fd 1:1:1 1:1:1, 1:1:1, 1:1:1, ITF402 FAT-B/E FAT-B/E B LC E Fd 1:1:1 1:1:1, 1:1:1, 1:1:1, ITF403 FAT-M/E FAT-M/E M LC E Fd 1:1:1 1:1:1, 1:1:1, 1:1:1,

3. Purification and Results

Cell culture supernatant was centrifuged followed by filtration. The filtered supernatant was loaded onto Monofinity A Resin Prepacked Column 1 ml (GenScript, Cat. No. L00433-11) at 1.0 ml/min. After a washing step, the antibodies were eluted and then buffer exchanged to PBS, pH 7.2. The antibodies were further purified by standard techniques. For example, some samples were further purified by size exclusion chromatography (SEC) using a Superdex 200 Increase 10/300 GL column or by ceramic hydroxyapatite chromatography using a CHT™ ceramic hydroxyapatite column (Bio-Rad). For other proteins, Protein A affinity chromatography was used for initial purification, followed by SEC if necessary.

Each of the expressed proteins was analyzed by SDS-PAGE under reducing and non-reducing conditions and Western blot analysis (using Goat Anti-Human IgG-HRP (GenScript, Cat. No. A00166), which showed that proteins and constituent chains had the desired molecular weights. Purity of the proteins was assessed using size-exclusion HPLC

Example 2

Nine of the sixteen different bispecific antibodies described in Example 1 were analyzed for binding to PD-1 on the surface of cells using flow cytometry. Cell lines used were CHO-Kl cells (negative control) and a CHO-Kl/PD-1 expressing. Antibodies used were an irrelevant human IgG (negative control), and commercially available anti-PD-1 (positive controls). The secondary antibody used was a goat anti Human IgG(H+L) iFluor 647 (1 μg/ml) (data not shown). In order to demonstrate concurrent binding of the bispecific molecules to PD1 and IL-1β, a sandwich FACS assay was performed. The binding curves are shown in FIG. 7. CHO cells expressing PD1 were bound by bispecific antibodies at the indicated concentrations. Unbound antibody was washed away and detection was performed using biotinylated IL-1β (2 ug/ml) followed by SA-iFluor 647 (1 ug/ml). Fluorescence intensity is indicative of both BiSAb immobilization on PD1+ cells and ability to concurrently bind IL-1β. Various combinations of anti-IL-1β VH/VL binding domains with two different pairs of anti-PD-1 VH/VL binding domains were formatted as BiS2, BiS3, FIT-IG or FAT-IG molecules. Of the constructs tested, the four binding molecules having anti-PD-1 VH/VL binding regions containing the CDR regions defined by the sequences of SEQ ID Nos: 1-6 all achieved a higher mean fluorescence intensity compared to the five binding molecules having anti-PD-1 VH/VL binding regions containing the CDR regions defined by the sequences of SEQ ID Nos: 6-12.

FIGS. 8-12 show additional binding data for additional binding proteins. FIG. 8 shows binding curves for binding of bispecific antibodies to cell membrane-bound PD-1 and soluble IL-1β simultaneously in a multiple-dose sandwich assay, as detected by flow cytometry. Variable binding affinities of the ITC, ITD and ITE series of bispecific antibodies are shown. All the binding affinities are substantially higher than control human IgG.

FIG. 9 shows binding curves for binding to cell membrane-bound PD-1 in a multiple-dose sandwich assay, as detected by flow cytometry. Variable binding affinities of the ITB and ITF series of bispecific antibodies are shown. All the binding affinities are substantially higher than control human IgG.

FIG. 10 shows binding curves for binding to cell membrane-bound PD-1 and soluble IL-1β simultaneously in a multiple-dose sandwich assay, as detected by flow cytometry. Variable binding affinities of ITB and ITF series of bispecific antibodies are shown. All the binding affinities are substantially higher than control human IgG.

FIG. 11 shows that bispecific antibodies block PD-1 activity in a PD-1/PD-L1 reporter assay. Variable blockade activities are shown for the ITA series of bispecific antibodies. All the blockade activies are substantially higher than control human IgG.

FIG. 12 shows that bispecific antibodies block IL-1β activity in a IL-1β functional assay. Variable blockade activities are demonstrated of the ITA series of bispecific antibodies. All the blockade activies are substantially higher than control human IgG. 

What is claimed is:
 1. A binding protein comprising a first binding domain and a second binding domain, wherein said first binding domain specifically binds and inhibits activation of PD-1 or PD-L1, and wherein said second binding domain specifically binds and inhibits the activity of IL-β or IL-1R.
 2. (canceled).
 3. The binding protein according to claim 1 wherein said binding domains are human immunoglobulin binding domains.
 4. The binding protein according to claim 1 wherein said binding protein comprises a third binding domain that specifically binds and inhibits activation of PD-1 or PD-L1 and a fourth binding domain that specifically binds and inhibits the activity of IL-β or IL-1R.
 5. (canceled)
 6. The binding protein according to claim 1 wherein said first binding domain comprises a) a heavy chain CDR1 of SEQ ID NO.:1; (b) a heavy chain CDR2 of SEQ ID NO.:2; (c) a heavy chain CDR3 of SEQ ID NO.:3; (d) a light chain CDR1 of SEQ ID NO.:4; (e) a light chain CDR2 of SEQ ID NO.:5; and (f) a light chain CDR3 of SEQ ID NO.:6.
 7. The binding protein according to claim 1 wherein said first binding domain comprises a) a heavy chain CDR1 of SEQ ID NO.:7; (b) a heavy chain CDR2 of SEQ ID NO.8; (c) a heavy chain CDR3 of SEQ ID NO.:9; (d) a light chain CDR1 of SEQ ID NO.:10; (e) a light chain CDR2 of SEQ ID NO.:11; and (f) a light chain CDR3 of SEQ ID NO.:12.
 8. The binding protein according to claim 1 wherein said first binding domain comprises a) a heavy chain CDR1 of SEQ ID NO.:13; (b) a heavy chain CDR2 of SEQ ID NO.14; (c) a heavy chain CDR3 of SEQ ID NO.:15; (d) a light chain CDR1 of SEQ ID NO.:16; (e) a light chain CDR2 of SEQ ID NO.:17; and (f) a light chain CDR3 of SEQ ID NO.:18.
 9. The binding protein according to claim 1 wherein said first binding domain comprises (a) a heavy chain CDR1 of SEQ ID NO.:19; (b) a heavy chain CDR2 of SEQ ID NO.:20; (c) a heavy chain CDR3 of SEQ ID NO.:21; (d) a light chain CDR1 of SEQ ID NO.:22; (e) a light chain CDR2 of SEQ ID NO.:23; and (f) a light chain CDR3 of SEQ ID NO.:24.
 10. The binding protein according to claim 1 5 wherein said first binding domain comprises (a) a heavy chain CDR1 of SEQ ID NO.:25; (b) a heavy chain CDR2 of SEQ ID NO.:26; (c) a heavy chain CDR3 of SEQ ID NO.:27; (d) a light chain CDR1 of SEQ ID NO.:28; (e) a light chain CDR2 of SEQ ID NO.:29; and (f) a light chain CDR3 of SEQ ID NO.:30.
 11. The binding protein according to claim 1, wherein said first binding domain comprises (a) a heavy chain CDR1 of SEQ ID NO.:31; (b) a heavy chain CDR2 of SEQ ID NO.:32; (c) a heavy chain CDR3 of SEQ ID NO.:33; (d) a light chain CDR1 of SEQ ID NO.:34; (e) a light chain CDR2 of SEQ ID NO.:35; and (f) a light chain CDR3 of SEQ ID NO.:36. 12-17. (canceled)
 18. The binding protein according to claim 1 wherein said second binding domain contain (a) a heavy chain CDR1 of SEQ ID NO.:49; (b) a heavy chain CDR2 of SEQ ID NO.:50; (c) a heavy chain CDR3 of SEQ ID NO.:51; (d) a light chain CDR1 of SEQ ID NO.:52, (e) a light chain CDR2 of SEQ ID NO.:53; and (f) a light chain CDR3 of SEQ ID NO.:54.
 19. (canceled)
 20. The binding protein according to claim 1, wherein said second binding domain contain (a) a heavy chain CDR1 of SEQ ID NO.:62 (b) a heavy chain CDR2 of SEQ ID NO.:63; (c) a heavy chain CDR3 of SEQ ID NO.:64; (d) a light chain CDR1 of SEQ ID NO.:65; (e) a light chain CDR2 of SEQ ID NO.:66; and (f) a light chain CDR3 of SEQ ID NO.:67.
 21. (canceled)
 22. The binding protein according to claim 1, wherein said first binding domain is an antibody binding domain that specifically binds and inhibits activation of PD-1 or PD-L1, and wherein said second binding domain comprises an interleukin-1β-binding domain of interleukin-1 receptor type 1 (IL-1R1) or interleukin-1 receptor type 2 (IL-1R2). 23-27. (canceled)
 28. The binding protein according to claim 22, wherein said interleukin-1β-binding domain of IL-1R1 further comprises IL-1R accessory protein.
 29. A method for the preparation of a binding protein according to claim 1, comprising the steps of a) transforming a host cell with vectors comprising nucleic acid molecules encoding said first binding domains and said second binding domain; b) culturing the host cell under conditions that allow synthesis of said binding protein; and c) recovering said binding protein from said culture.
 30. A host cell comprising vectors comprising nucleic acid molecules encoding the first binding domain and second binding domain according to claim
 1. 31. A pharmaceutical composition comprising a binding protein according to claim 1 and a pharmaceutically acceptable excipient.
 32. A method of treating cancer in a subject comprising administering a binding protein according to claim 1 to a subject in need thereof.
 33. (canceled)
 34. A bispecific binding protein comprising a first protein chain, a second protein chain and a third protein chain, wherein said first protein chain comprises a heavy chain comprising VH, CH1, CH2, and CH3 domains, and further comprises a first Fab domain (Fab1) at a solvent exposed loop in the CH2 domain, the CH3 domain, or at the interface of the CH2 and CH3 domains; wherein said second chain comprises a second Fab domain and wherein said third chain comprises a third Fab domain; wherein said second chain Fab domain associates with the VH and CH1 domains of said first protein chain to form a first binding domain, and wherein said third chain Fab domain associates with the first Fab domain at the solvent exposed loop in said first protein to form a second binding domain. 35-48. (canceled)
 49. A bispecific binding protein according to claim 34, wherein said first binding domain binds specifically to PD-1 or PD-L1 and said second binding domain binds specifically to IL-10 or IL-1R, or said first binding domain binds specifically to IL-1β or IL-1R and said second binding domain binds specifically to PD-1 or PD-L1. 50-52. (canceled)
 53. A pharmaceutical composition comprising the binding protein according to claim 34 and a pharmaceutically acceptable carrier.
 54. A method for the preparation of a binding protein according to claim 34, comprising the steps of a) transforming a host cell with vectors comprising nucleic acid molecules encoding said first, second and third protein chains; b) culturing the host cell under conditions that allow synthesis of said binding protein; and c) recovering said binding protein from said culture.
 55. A host cell comprising vectors comprising nucleic acid molecules encoding said first, second and protein chain according to claim
 34. 56. A method of treating cancer in a subject comprising administering a binding protein according to claim 34 to a subject in need thereof. 57-69. (canceled)
 70. A method of preventing or reducing the risk of cancer in a subject at risk thereof, comprising administering to said subject an effective amount of a binding protein according to claim
 1. 71-76. (canceled) 